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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE KDM2A-H3K36ME-NO COMPLEX
 
Authors :  Z. Cheng
Date :  03 Jun 14  (Deposition) - 13 May 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Cheng, P. Cheung, A. J. Kuo, E. T. Yukl, C. M. Wilmot, O. Gozani, D. J. Patel
A Molecular Threading Mechanism Underlies Jumonji Lysine Demethylase Kdm2A Regulation Of Methylated H3K36.
Genes Dev. V. 28 1758 2014
PubMed-ID: 25128496  |  Reference-DOI: 10.1101/GAD.246561.114

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 2A
    ChainsA, C
    EC Number1.14.11.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 36-364
    GeneKDM2A, FBXL11, JHDM1A, KIAA1004
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymF-BOX AND LEUCINE-RICH REPEAT PROTEIN 11,F-BOX/LRR-REPEAT PROTEIN 11,JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A, [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A
 
Molecule 2 - LYSINE-SPECIFIC DEMETHYLASE 2A
    ChainsB, D
    EC Number1.14.11.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 450-517
    GeneKDM2A, FBXL11, JHDM1A, KIAA1004
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymF-BOX AND LEUCINE-RICH REPEAT PROTEIN 11,F-BOX/LRR-REPEAT PROTEIN 11,JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A, [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A
 
Molecule 3 - PEPTIDE
    ChainsE, F
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCHEMICALLY SYNTHESIZED PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB  E 
Biological Unit 2 (1x)  CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2MLZ2Mod. Amino AcidN-METHYL-LYSINE
3NO1Ligand/IonNITRIC OXIDE
4SIN2Ligand/IonSUCCINIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MLZ1Mod. Amino AcidN-METHYL-LYSINE
3NO-1Ligand/IonNITRIC OXIDE
4SIN1Ligand/IonSUCCINIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MLZ1Mod. Amino AcidN-METHYL-LYSINE
3NO-1Ligand/IonNITRIC OXIDE
4SIN1Ligand/IonSUCCINIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:212 , ASP A:214 , HIS A:284 , NO A:602 , SIN A:603binding site for residue FE A 601
2AC2SOFTWAREHIS A:212 , ASP A:214 , FE A:601 , SIN A:603 , MLZ E:36binding site for residue NO A 602
3AC3SOFTWAREASN A:142 , THR A:209 , HIS A:212 , TYR A:222 , LYS A:229 , HIS A:284 , VAL A:286 , FE A:601 , NO A:602 , MLZ E:36binding site for residue SIN A 603
4AC4SOFTWAREHIS C:212 , ASP C:214 , HIS C:284 , SIN C:602binding site for residue FE C 601
5AC5SOFTWAREASN C:142 , ILE C:144 , THR C:209 , HIS C:212 , TYR C:222 , LYS C:229 , HIS C:284 , VAL C:286 , FE C:601 , MLZ F:36binding site for residue SIN C 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TN7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4TN7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TN7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TN7)

(-) Exons   (0, 0)

(no "Exon" information available for 4TN7)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........ee.hhhhhhhhhhhhhh....eee...............hhhhhhhhhh...eeeeee.....eeeeehhhhhhhhh.........eeeeeee.....hhhhh..hhhhhhhhhhhhh.hhhhhh...................eeeee....eeeee.hhhhheeeeeeee..eeeeee..hhhhhhhhhhhhhhh.....hhhhhh...eeeee....eeee....eeeee....eeeeeeee....hhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tn7 A  36 RTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDME 364
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355         

Chain B from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhh...hhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4tn7 B 450 QVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELASSDPKLALTGVPIVQWP 517
                                   459       469       479       489       499       509        

Chain C from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........ee.hhhhhhhhhhhhhh....eee...............hhhhhhhhhh...eeeeee....eeeeeehhhhhhhhhh........eeeeeee.....hhhhh..hhhhhhhhhhhhh.hhhhhh...................eeeee....eeeee.hhhhheeeeeeee..eeeeee..hhhhhhhhhhhhhhhhhhh..........eeeee....eeee....eeeee....eeeeeeee....hhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tn7 C  36 RTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDME 364
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355         

Chain D from PDB  Type:PROTEIN  Length:68
                                                                                                    
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhh...hhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 4tn7 D 450 QVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELASSDPKLALTGVPIVQWP 517
                                   459       469       479       489       499       509        

Chain E from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4tn7 E  29 APATGGVkKP  38
                                   |38
                                  36-MLZ

Chain F from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4tn7 F  29 APATGGVkKP  38
                                   |38
                                  36-MLZ

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4TN7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TN7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TN7)

(-) Gene Ontology  (51, 54)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        KDM2A_MOUSE | P599974qwn 4qx7 4qx8 4qxb 4qxc 4qxh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4TN7)